机器学习和生物信息学实验室联盟

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微生物数据分析组工作与成果

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发表于 2022-7-3 08:53:30 | 显示全部楼层 |阅读模式
研究方向
  • Microbiome in human health and diseases (oral, gut)
  • Microbial ecology of natrual habitats (hot springs)
  • Identify biomolecules of microorganisms (non-coding DNA, miRNAs, secreted proteins, etc.)

研究成员

  • 邹 权 (教授,电子科技大学)
  • 马占山(研究员,中国科学院昆明动物研究所)
  • 王彦苏(博士后,电子科技大学)
  • 杨凤龙 (副教授,福建医科大学)
  • 王 超 (副教授,成都信息工程大学)

承担项目
  • 个体化肠道菌群代谢网络的建模方法研究及应用,国家自然科学基金青年基金,62102065,杨凤龙主持
  • 从宏基因组重建细菌全基因组单倍型,国家自然科学基金青年基金,62102068,曹晨主持
  • 基于机器学习方法的土传真菌病害预测研究,国家自然科学基金青年基金,62102269,王彦苏主持


网站与数据库

  • mAML (Automated machine learning pipeline with a microbiome repository for human disease classification)
  • GutBalance (Human gut microbiome-based disease prediction and biomarker discovery with compositionality addressed)
  • Sc-ncDNAPred (Identification of non-coding DNA in Saccharomyces cerevisiae)
  • NonClasGP-Pred (Prediction of non-classically secreted proteins)
  • MDADP(integrating database and prediction tools for microbe-disease associations)

发表论文

  • Yong Huang, Quan Zou, Xing Jia Shen, Xue Li Yu,Zhan Bin Wang, Xiang Chao Cheng. Constructionof baculovirus expression vector of miRNAs and its expression in insect cells. Molecular Genetics, Microbiology and Virology. 2012, 27(2)85-90
  • Hongju Chen, Shuting Peng, Lin Dai, Quan Zou, Bin Yi, Xianghong Yang, Zhanshan (Sam) Ma. Oralmicrobial community assembly under the influence of periodontitis. PLoS One. 2017,12(8): e0182259
  • Wenying He, Ying Ju, Xiangxiang Zeng, Xiangrong Liu*, Quan Zou*. Sc-ncDNAPred: Asequence-based predictor for identifying non-coding DNA in Saccharomycescerevisiae. Frontiers in Microbiology.2018, 9: 2174.(web server)
  • Kaiyang Qu, Fei Guo, Xiangrong Liu, Yuan Lin*, Quan Zou*. Application of MachineLearning in Microbiology. Frontiers inMicrobiology. 2019, 10: 827
  • Lianwei Li, Wendy Li, Quan Zou*, Zhanshan(Sam) Ma*. Network analysis of the hot spring microbiome sketches out possible niche differentiations among ecological guilds. Ecological Modelling. 2020, 431: 109147
  • Fenglong Yang, Quan Zou*. mAML: an automated machine learning pipeline with a microbiome repository for human disease classification. DATABASE-The Journal of Biological Databases and Curation. 2020, 2020: baaa050. (web)
  • Fenglong Yang, Quan Zou*, Bo Gao*. GutBalance: a server for the human gut microbiome-based disease prediction and biomarker discovery with compositionality addressed. Briefings in Bioinformatics. 2021, 22(5):bbaa436. (web site)
  • Fenglong Yang, Quan Zou*. DisBalance: a platform to automatically build balance-based disease prediction models and discover microbial biomarkers from microbiome data. Briefings in Bioinformatics. 2021, 22(5):bbab094 (web)
  • Wendy Li, Yang Sun, Lin Dai, Hongju Chen, Bin Yi, Junkun Niu, Lan Wang, Fengrui Zhang, Juan Luo, Kunhua Wang, Rui Guo, Lianwei Li, Quan Zou, Zhanshan (Sam) Ma, Yinglei Miao. Ecological and network analyses identify four microbial species with potential significance for the diagnosis/treatment of ulcerative colitis (UC). BMC Microbiology. 2021, 21: 138
  • Chao Wang, Quan Zou*. A Machine Learning Method for Differentiating and Predicting Human-Infective Coronavirus Based on Physicochemical Features and Composition of the Spike Protein. Chinese Journal of Electronics. 2021, 30(5): 815-823 (data and software)
  • Chunyan Ao, Yu Zhang, Dapeng Li, Yuming Zhao*, Quan Zou*. Progress in the developmentof antimicrobial peptide prediction tools. Currentprotein & peptide science. 2021, 22(3): 211-216
  • Lei Wang, Hao Li*, Yuqi Wang, Yihong Tan, Zhiping Chen, Tingrui Pei, Quan Zou*. MDADP: A webserver integrating database and prediction tools for microbe-disease associations. IEEE Journal of Biomedical and Health Informatics. 2022, 26(7): 3427-3434 (web)
  • Yansu Wang, Jie Wu,Jiacheng Yan, Ming Guo, Lei Xu, Liping Hou*, Quan Zou*. Comparativegenome analysis of plant ascomycete fungal pathogens with different lifestylesreveals distinctive virulence strategies. BMC Genomics. 2022, 23:34 (web)
  • Yansu Wang, Ximei Luo, QuanZou*. Effector-GAN: prediction of fungal effector proteins based onpretrained deep representation learning methods and generative adversarialnetworks. Bioinformatics. Doi: 10.1093/bioinformatics/btac374. (web server)
  • Zilong Zhang, Feifei Cui, Chen Cao, Qingsuo Wang*, QuanZou*. Single-cell RNA analysis reveals the potential risk of organ-specificcell types vulnerable to SARS-CoV-2 infections. Computers in Biology andMedicine. 2022, 140: 105092
  • Mengting Niu, Ying Ju,Chen Lin*, Quan Zou*. Characterizing Viral circRNAs and theirApplication in Identifying CircRNAs in Viruses. Briefings in Bioinformatics. 2022, 23(1): bbab404. (web server)




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